Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 5211054 Shew_3470 isopropylmalate isomerase large subunit (RefSeq)
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__PV4:5211054 Length = 466 Score = 236 bits (602), Expect = 1e-66 Identities = 157/439 (35%), Positives = 222/439 (50%), Gaps = 54/439 (12%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVRE 64 VD + H+ TS A + K + ++ P + DH + + L R V Sbjct: 27 VDRHLVHEVTSPQAFSGLK-VAGRKLRAPEKTFATMDHNTSTKSASLDALSPMARTQVET 85 Query: 65 --QSIPNF----YEI---GEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVG 115 Q+ F Y+I +GI H + PE G LPG ++V DSH+ T+GAFGA A G+G Sbjct: 86 LAQNCKEFGVRLYDIHHKNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIG 145 Query: 116 ATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYG 175 +++ + AT L ++ ++ V G + + AKD+ L +IGK G+ G T VEF G Sbjct: 146 TSEVEHVMATQTLRQLKAKTMKIEVRGLVADGITAKDIVLAIIGKIGMDGGTGYVVEFCG 205 Query: 176 QAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNR-----------AVAPYEPV 224 +AI+ LS+ GRMT+CNMAIEMGAK G++ PD+ T D+L+ R AVA ++ + Sbjct: 206 EAIAALSMEGRMTVCNMAIEMGAKAGMIAPDQTTIDYLEGREFAPKGEAWQQAVAAWKAL 265 Query: 225 YSDPDASYLKEFVYDAGDIEPQV--------------ACPHQVDNVKP------------ 258 SD DA + V +A DI PQ+ P+ D P Sbjct: 266 KSDEDAMFDAHVVLEASDIAPQLTWGTNPGQVVAIDQCVPNPEDETNPTVKASIEKALDY 325 Query: 259 VGEVEGTH-----VDQVFIGTCTNGRLEDLEVAASVLKGKKVT--VRTIIIPASRSTLLA 311 V GT +++VFIG+CTN R+EDL AA KG+KV V I++P S Sbjct: 326 VALTPGTQMTDVSINKVFIGSCTNSRIEDLRSAAQQAKGRKVAAGVTAIVVPGSGLVKEQ 385 Query: 312 AIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLA 371 A G +I + AG PGC CL + L G+ C ST+NRNF+GR G+ +L Sbjct: 386 AEAEGLDKIFIDAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLV 445 Query: 372 SPATAAASALTGEITDPRK 390 SPA AAA+A+ G D RK Sbjct: 446 SPAMAAAAAIAGHFVDIRK 464 Lambda K H 0.318 0.135 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 428 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 391 Length of database: 466 Length adjustment: 32 Effective length of query: 359 Effective length of database: 434 Effective search space: 155806 Effective search space used: 155806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory